Description Usage Arguments Details Author(s) See Also
View source: R/patchwork.copynumbers.r
Input data for this function should be assessed from any of the karyotype_chroms() plots. For example <yoursample>_karyotype.chr<1-22,X,Y>.png.
See argument details.
1 | patchwork.copynumbers(CNfile,cn2,delta,het,hom,maxCn=8,ceiling=1,forcedelta=F,male.sample=F,male2femref=F)
|
CNfile |
The name and path of your copynumbers file, generated from patchwork.plot(). Example Myfile_copynumbers.Rdata. |
cn2 |
The approximate position of copy number 2,diploid, on total intensity / coverage axis. |
delta |
The difference in total intensity between consecutive copy numbers. For example 1 and 2 or 2 and 3. If copy number 2 has total intensity ~0.6 and copy number 3 har total intensity ~0.8 then delta would be 0.2. |
het |
Allelic imbalance ratio of heterozygous copy number 2. |
hom |
Allelic imbalance ratio of Loss-of-heterozygosity copy number 2. |
maxCn |
Highest copy number to calculate for. Default is 8. |
ceiling |
Default is 1. |
forcedelta |
Default is FALSE. If TRUE the delta value will not be subject to small adjustment changes. |
male.sample |
Default is FALSE. If it is a male sample put TRUE here and it will handle the XY chromosomes better. |
male2femref |
Default is FALSE. If TRUE the sample is male but the reference you used is female. This will correct for this. |
1. Run the patchwork.plot correctly. This will generate <yourfile>_copynumbers.Rdata. 2. View your plots and decide the correct parameters for the other arguments of this function. 4. Run the function.
Markus Mayrhofer, markus.mayrhofer@medsci.uu.se Sebastian DiLorenzo, sebastian.dilorenzo@medsci.uu.se
patchwork.plot
subfunctions_copynumbers
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